<li><a href="#processingalignments">Processing alignments</a></li>
<li><a href="#outputtingalignmentfiles">Outputting alignment files</a></li>
<li><a href="#exportingimagefiles">Exporting image files</a></li>
- <li><a href="#exporting3dstructureimagefiles">Exporting 3D structure image files</a></li>
<li><a href="#controllingflowofarguments">Controlling flow of arguments</a></li>
</ul>
<tr valign="top"><td><code>‑‑help‑all</code></td><td>Help for all arguments</td></tr>
<tr valign="top">
- <td><code>‑‑headless / ‑‑noheadless</code></td>
- <td>Run Jalview in headless (/ or not in headless) mode. In headless mode, no GUI interface will be created and Jalview will quit after all arguments have been processed.
+ <td><code>‑‑headless</code></td>
+ <td>Run Jalview in headless mode. In headless mode, no GUI interface will be created and Jalview will quit after all arguments have been processed.
<br/>
- If you use a command line argument to specify an output file of some kind (<code>--output</code>, <code>--image</code> or <code>--structureimage</code>) then <strong>headless mode will be assumed</strong>. If you don't want this behaviour use <code>--noheadless</code> or <code>--gui</code>.
+ If you use a command line argument to specify an output file of some kind (<code>‑‑output</code>, <code>‑‑image</code> or <code>‑‑structureimage</code>) then <strong>headless mode will be assumed</strong>. If you don't want this behaviour use <code>‑‑gui</code>.
</td>
</tr>
<tr valign="top">
<td><code>‑‑gui</code></td>
- <td>Force Jalview to run in graphical mode. This can be used to counter the assumption of headless mode when an argument that creates an output file is used. <code>--gui</code> takes precedence over <code>--headless</code>.</td>
+ <td>Force Jalview to run in graphical mode. This can be used to counter the assumption of headless mode when an argument that creates an output file is used. <code>‑‑gui</code> takes precedence over <code>‑‑headless</code>.</td>
</tr>
<tr valign="top">
</tr>
<tr valign="top">
+ <td><code>‑‑javaconsole / ‑‑nojavaconsole</code></td>
+ <td>Show (/ or don't show) the Java Console. Using one of these overrides any saved Preference.</td>
+ </tr>
+
+ <tr valign="top">
<td><code>‑‑questionnaire / ‑‑noquestionnaire</code></td>
<td>Show (/ or don't show) the questionnaire if one is available.</td>
</tr>
<code>phylip</code> (<code>phy</code>),
<br/>
<code>jalview</code> (<code>jvp, jar</code>).
+ <br/>
+ To output directly to STDOUT (console output) use the filename <code>-</code> (a single hyphen). In this case all STDOUT messages will instead go to STDERR. If no <code>format</code> is supplied then Fasta will be assumed.
</td>
<td><code>format=<em>name</em></code></td>
<td align="center">✓</td>
<td align="center">✓</td>
</tr>
+ <tr valign="top">
+ <td><code>‑‑mkdirs</code></td>
+ <td>Enable automatic creation of new directories and parent directories for filenames given, or created through substitutions, in <code>‑‑output</code>, <code>‑‑image</code> or <code>‑‑structureimage</code> arguments.
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+
+Automatically create directories when outputting a file to a new directory
</table>
<code>biojs</code>.
</td>
<td>
- <code>type=<em>name</em>,
- <code>textrenderer=<em>name</em>,
- <code>scale=<em>number</em>,
- <code>width=<em>number</em>,
- <code>height=<em>number</em>
+ <code>
+ type=<em>name</em>,
+ <br/>
+ textrenderer=<em>name</em>,
+ <br/>
+ scale=<em>number</em>,
+ <br/>
+ width=<em>number</em>,
+ <br/>
+ height=<em>number</em>,
+ <br/>
+ imagecolour=<em>name</em>
+ </code>
+ </td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑structureimage <em>filename</em></code></td>
+ <td>Export an image of a 3D structure opened in JMOL (currently jmol only). Each <code>‑‑structureimage</code> filename will output a file for each <code>‑‑structureimage</code> that has been applied to the open alignment window. In this situation, to avoid overwriting the same file with each structure, additional substitutions <code>{structuredirname}</code>, <code>{structurebasename}</code> and <code>{structureextname}</code> are available being substituted with the directory path, file basename and file extension of each structure file. Image formats can be:
+ <br/>
+ <code>svg</code>,
+ <br/>
+ <code>png</code>,
+ <br/>
+ <code>eps</code>.
+ </td>
+ <td>
+ <code>
+ type=<em>name</em>,
+ <br/>
+ textrenderer=<em>name</em>,
+ <br/>
+ scale=<em>number</em>,
+ <br/>
+ width=<em>number</em>,
+ <br/>
+ height=<em>number</em>,
+ <br/>
+ imagecolour=<em>name</em>
+ <br/>
+ bgcolour=<em>name</em>
+ </code>
</td>
<td align="center">✓</td>
</tr>
<tr valign="top">
<td><code>‑‑type <em>name</em></code></td>
- <td>Set the image format for the preceding <code>‑‑image</code> to <em>name</em>. Valid values for <em>name</em> are:
+ <td>Set the image format for the preceding <code>‑‑image</code> or <code>‑‑structureimage</code> to <em>name</em>. Valid values for <em>name</em> are:
<br/>
<code>svg</code>,
<br/>
<tr valign="top">
<td><code>‑‑textrenderer <em>name</em></code></td>
- <td>Sets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Valid values for <em>name</em> are:
+ <td>Sets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Applies to the preceding <code>‑‑image</code> or <code>‑‑structureimage</code>. Valid values for <em>name</em> are:
<br/>
<code>text</code>,
<br/>
<tr valign="top">
<td><code>‑‑scale <em>number</em></code></td>
- <td>Sets a scaling for bitmap image format (PNG). Should be given as a floating point number. This can also be set as a sub-value modifier to the <code>--image</code> value. If used in conjunction with <code>--width</code> and <code>--height</code> then the smallest scaling will be used (<code>scale</code>, <code>width</code> and <code>height</code> provide bounds for the image).
+ <td>Sets a scaling for bitmap image format (PNG). Should be given as a floating point number. Applies to the preceding <code>‑‑image</code> or <code>‑‑structureimage</code>. This can also be set as a sub-value modifier to the <code>‑‑image</code> or <code>‑‑structureimage</code> value. If used in conjunction with <code>‑‑width</code> and <code>‑‑height</code> then the smallest size will be used (<code>scale</code>, <code>width</code> and <code>height</code> provide bounds for the image).
</td>
<td></td>
<td align="center">✓</td>
<tr valign="top">
<td><code>‑‑width <em>number</em></code></td>
- <td>Sets a width for bitmap image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. This can also be set as a sub-value modifier to the <code>--image</code> value. If used in conjunction with <code>--scale</code> and <code>--height</code> then the smallest scaling will be used (<code>scale</code>, <code>width</code> and <code>height</code> provide bounds for the image).
+ <td>Sets a width for bitmap image format (PNG) with the height maintaining the aspect ratio. Applies to the preceding <code>‑‑image</code> or <code>‑‑structureimage</code>. Should be given as a positive integer. This can also be set as a sub-value modifier to the <code>‑‑image</code> or <code>‑‑structureimage</code> value. If used in conjunction with <code>‑‑scale</code> and <code>‑‑height</code> then the smallest size will be used (<code>scale</code>, <code>width</code> and <code>height</code> provide bounds for the image).
</td>
<td></td>
<td align="center">✓</td>
<tr valign="top">
<td><code>‑‑height <em>number</em></code></td>
- <td>Sets a height for bitmap image format (PNG) with the width maintaining the aspect ratio. Should be given as a positive integer. This can also be set as a sub-value modifier to the <code>--image</code> value. If used in conjunction with <code>--scale</code> and <code>--width</code> then the smallest scaling will be used (<code>scale</code>, <code>width</code> and <code>height</code> provide bounds for the image).</td>
+ <td>Sets a height for bitmap image format (PNG) with the width maintaining the aspect ratio. Applies to the preceding <code>‑‑image</code> or <code>‑‑structureimage</code>. Should be given as a positive integer. This can also be set as a sub-value modifier to the <code>‑‑image</code> or <code>‑‑structureimage</code> value. If used in conjunction with <code>‑‑scale</code> and <code>‑‑width</code> then the smallest size will be used (<code>scale</code>, <code>width</code> and <code>height</code> provide bounds for the image).</td>
<td></td>
<td align="center">✓</td>
</tr>
<tr valign="top">
- <td><code>‑‑groovy <em>filename</em></code></td>
- <td>Process a groovy script in the file for the open alignment.</td>
+ <td><code>‑‑bgcolour <em>name</em></code></td>
+ <td>Only applies to structure images (opened with <code>jmol</code> structure viewer). Sets the background colour of the preceding <code>‑‑structureimage</code>. <em>name</em> should be either a named colour (e.g. <code>white</code>, <code>cyan</code>) known to Jmol, or can be given as a six digit RGB hex string (e.g. <code>ffffff</code>, <code>00ffff</code>). This can also be set as a sub-value modifier to the <code>‑‑structureimage</code> value.</td>
<td></td>
<td align="center">✓</td>
</tr>
- </table>
-
-
- <h2><a name="exporting3dstructureimagefiles"></a>Exporting 3D structure image files (<code>jmol</code> only)</h2>
-
- <table border="1" cellpadding="3">
- <tr valign="top">
- <td><strong>argument</strong></td>
- <td><strong>action</strong></td>
- <td><strong>sub-value modifiers</strong> (optional)</td>
- <td><strong>linked</strong> (optional)</td>
- </tr>
-
<tr valign="top">
- <td><code>‑‑structureimage <em>filename</em></code></td>
- <td>Export an image of a 3D structure opened in JMOL. Image formats can be:
- <br/>
- <code>svg</code>,
- <br/>
- <code>png</code>,
- <br/>
- <code>eps</code>.
- </td>
- <td>
- <code>structureimagetype=<em>name</em>,
- <code>structureimagetextrenderer=<em>name</em>,
- <code>structureimagescale=<em>number</em>,
- <code>structureimagewidth=<em>number</em>,
- <code>structureimageheight=<em>number</em>
- </td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑structureimagetype <em>name</em></code></td>
- <td>Set the structure image format for the preceding --structureimage. Valid values are:
- <br/>
- <code>svg</code>,
- <br/>
- <code>png</code>,
- <br/>
- <code>eps</code>.
- </td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑structureimagetextrenderer <em>name</em></code></td>
- <td>Sets whether text in a vector structure image format (SVG, EPS) should be rendered as text or vector line-art. Possible values are:
- <br/>
- <code>text</code>,
- <br/>
- <code>lineart</code>.
- </td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑structureimagescale <em>number</em></code></td>
- <td>Sets a scaling for bitmap structure image format (PNG). Should be given as a floating point number. If used in conjunction with --structureimagewidth and --structureimageheight then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).
- </td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑structureimagewidth <em>number</em></code></td>
- <td>Sets a width for bitmap structure image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --structureimagescale and --structureimageheight then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).
- </td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
- <tr valign="top">
- <td><code>‑‑structureimageheight <em>number</em></code></td>
- <td>Sets a height for bitmap structure image format (PNG) with the width maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --structureimagescale and --structureimagewidth then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).
- </td>
+ <td><code>‑‑groovy <em>filename</em></code></td>
+ <td>Process a groovy script in the file for the open alignment.</td>
<td></td>
<td align="center">✓</td>
</tr>
<td>
Move on to a new alignment window. This will ensure <code>‑‑append</code> will start a new alignment window and other linked arguments will apply to the new alignment window.
<br/>
- <em>Note</em> that <code>--open</code> already starts a new alignment window for each file it opens.
+ <em>Note</em> that <code>‑‑open</code> already starts a new alignment window for each file it opens.
</td>
</tr>
<tr valign="top">
<td><code>‑‑substitutions / ‑‑nosubstitutions</code></td>
<td>The following argument values allow (or don't allow) subsituting filename parts. This is initially true. Valid substitutions are
+ <br/>
<code>{basename}</code> - the filename-without-extension of the currently <code>‑‑open</code>ed file (or first <code>‑‑append</code>ed file),
<br/>
<code>{dirname}</code>, - the directory (folder) name of the currently <code>‑‑open</code>ed file (or first <code>‑‑append</code>ed file),
+ <code>{extension}</code>, - the extension of the filename of the currently <code>‑‑open</code>ed file (or first <code>‑‑append</code>ed file),
<br/>
<code>{argfilebasename}</code> - the filename-without-extension of the current <code>‑‑argfile</code>,
<br/>
<code>{argfiledirname}</code> - the directory (folder) name of the current <code>‑‑argfile</code>,
<br/>
+ <code>{structurebasename}</code> - the filename-without-extension of the <code>‑‑structure</code> file. Only available to <code>‑‑structureimage</code> .
+ <br/>
+ <code>{structuredirname}</code>, - the directory (folder) name of the <code>‑‑structure</code> file. Only available to <code>‑‑structureimage</code> .
+ <br/>
+ <code>{structureextension}</code>, - the extension of the filename of the <code>‑‑structure</code> file. Only available to <code>‑‑structureimage</code> .
+ <br/>
<code>{n}</code> - the value of the index counter (starting at 0).
<br/>
- <code>{++n}</code> - increase and substitute the value of the index counter,
+ <code>{++n}</code> - increase and substitute the value of the index counter.
+ <br/>
+ <code>{m}</code> - the value of the on-the-fly counter (starting at 0). Only available to <code>‑‑structureimage</code> .
+ <br/>
+ <code>{++m}</code> - increase and substitute the (incremented) value of the on-the-fly counter. Only available to <code>‑‑structureimage</code> .
<br/>
<code>{}</code> - the value of the current alignment window <em>default</em> index.
</td>
<tr valign="top">
<td><code>‑‑allstructures / ‑‑noallstructures</code></td>
<td>
- Apply (or stop applying) the following 3D structure formatting arguments to all structures <em>within the current open alignment</em>. Whilst <code>--allstructures</code> will continue to operate for a <code>--new</code> alignment, the structure formatting arguments must be set again for each new alignment.
+ Apply (or stop applying) the following 3D structure formatting arguments to all structures <em>within the current open alignment</em>. Whilst <code>‑‑allstructures</code> will continue to operate for a <code>‑‑new</code> alignment, the structure formatting arguments must be set again for each new alignment.
</td>
</tr>
git://source.jalview.org / jalview.git / blobdiff